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- PDB-4mo0: Crystal structure of aIF1 from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 4mo0
TitleCrystal structure of aIF1 from Methanocaldococcus jannaschii
ComponentsProtein translation factor SUI1 homolog
KeywordsTRANSLATION / alpha-beta domain
Function / homology
Function and homology information


translation reinitiation / formation of translation preinitiation complex / translation initiation factor activity / regulation of translation
Similarity search - Function
Translation factor SUI1 homolog, archaea / Archaeal/bacterial translation initiation factor SUI1 / : / SUI1-like domain / Translation Initiation Factor Eif1 / SUI1 domain superfamily / Translation initiation factor SUI1 / Translation initiation factor SUI1 family profile. / SUI1 domain / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein translation factor SUI1 homolog
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.1 Å
AuthorsSchmitt, E. / Mechulam, Y.
CitationJournal: To be Published
Title: Crystal structure of aIF1 from Methanocaldococcus jannaschii
Authors: Coureux, P.-D. / Schmitt, E. / Monestier, A. / Larquet, E. / Cladiere, L. / Menetret, J.-F. / Klaholz, B. / Mechulam, Y.
History
DepositionSep 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein translation factor SUI1 homolog


Theoretical massNumber of molelcules
Total (without water)11,6221
Polymers11,6221
Non-polymers00
Water68538
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.440, 51.440, 146.060
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-206-

HOH

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Components

#1: Protein Protein translation factor SUI1 homolog / aIF1


Mass: 11621.787 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0463, sui1 / Plasmid: pet15blpa / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q57902
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.75 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25% PEG3350, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 16, 2010
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.1→32.9 Å / Num. all: 7257 / Num. obs: 7272 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.7 % / Biso Wilson estimate: 38.7 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.032
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 17.9 % / Rmerge(I) obs: 0.595 / Mean I/σ(I) obs: 5.5 / Num. unique all: 905 / Rsym value: 0.578 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.1→32.866 Å / SU ML: 0.44 / σ(F): 1.38 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2279 339 4.7 %RANDOM
Rwork0.22 ---
obs0.2203 7214 99.24 %-
all-7257 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.946 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 46.54 Å2
Baniso -1Baniso -2Baniso -3
1-3.8036 Å2-0 Å2-0 Å2
2--3.8036 Å2-0 Å2
3----7.6071 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms627 0 0 38 665
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008632
X-RAY DIFFRACTIONf_angle_d1.073838
X-RAY DIFFRACTIONf_dihedral_angle_d18.412252
X-RAY DIFFRACTIONf_chiral_restr0.06998
X-RAY DIFFRACTIONf_plane_restr0.003104
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.64580.25891760.23413333X-RAY DIFFRACTION100
2.6458-32.87030.21961630.21643542X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 1.5593 Å / Origin y: 14.6822 Å / Origin z: 6.4597 Å
111213212223313233
T0.1993 Å20.0178 Å20.0282 Å2-0.3356 Å20.112 Å2--0.2675 Å2
L3.3137 °2-2.1789 °21.8248 °2-3.2909 °2-1.2279 °2--4.0659 °2
S0.0648 Å °-0.0089 Å °0.0874 Å °0.0616 Å °0.0814 Å °0.045 Å °-0.0286 Å °-0.1461 Å °-0.1143 Å °
Refinement TLS groupSelection details: all

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